Sorry, I think I’ve done a poor job at explaining this. To start at the beginning, my issues arose because I am trying to interface with an external Flash chip over SPI using SPI.h provided in the Arduino IDE. That wasn’t working as it should, so I probed some things and saw low SPI voltages on the pins. I broke out the CS and saw that when it is connected to the Flash chip, it is only reading a high of 2.0V (the voltage supplied to the chip looks good at about 3.2V). The 2.0V is well outside of tolerance however. I have configured the CS as an output and manually write it high and low, so I can watch it go between 0V and 2.0V. If I change the jumper to the 5V side, I can increase this to 2.4V.
To answer mwachs5’s question, there are actually two sample code things in the OP (i.e. two separate test binaries). They occur in the setup() function and I am probing during loop(). What was meant is that as far as I can tell, configuring a pin as an input is equivalent (in terms of output voltage) as configuring a pin as output and writing it high when it is connected to an LED (in this case).
I think the issue is that because of the “smart” pull-ups, it is trying to decrease current draw, but inadvertantly changing the signalling voltage, which is causing SPI to fail.